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- PDB-7zh7: Cryo-EM structure of ex vivo AA amyloid from renal tissue of a sh... -

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Basic information

Entry
Database: PDB / ID: 7zh7
TitleCryo-EM structure of ex vivo AA amyloid from renal tissue of a short hair cat deceased in a shelter
ComponentsSerum amyloid A proteinSerum amyloid A
KeywordsPROTEIN FIBRIL / AA amyloidosis / cat / Serum amyloid A
Function / homologySerum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / high-density lipoprotein particle / acute-phase response / Serum amyloid A protein
Function and homology information
Biological speciesFelis catus (domestic cat)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSchulte, T. / Chaves-Sanjuan, A. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Health Italy
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of ex vivo fibrils associated with extreme AA amyloidosis prevalence in a cat shelter.
Authors: Tim Schulte / Antonio Chaves-Sanjuan / Giulia Mazzini / Valentina Speranzini / Francesca Lavatelli / Filippo Ferri / Carlo Palizzotto / Maria Mazza / Paolo Milani / Mario Nuvolone / Anne- ...Authors: Tim Schulte / Antonio Chaves-Sanjuan / Giulia Mazzini / Valentina Speranzini / Francesca Lavatelli / Filippo Ferri / Carlo Palizzotto / Maria Mazza / Paolo Milani / Mario Nuvolone / Anne-Cathrine Vogt / Monique Vogel / Giovanni Palladini / Giampaolo Merlini / Martino Bolognesi / Silvia Ferro / Eric Zini / Stefano Ricagno /
Abstract: AA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at ...AA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at high SAA serum levels during chronic inflammation. Prion-like transmission was reported as possible cause of extreme AA amyloidosis prevalence in captive animals, e.g. 70% in cheetah and 57-73% in domestic short hair (DSH) cats kept in zoos and shelters, respectively. Herein, we present the 3.3 Å cryo-EM structure of AA amyloid extracted post-mortem from the kidney of a DSH cat with renal failure, deceased in a shelter with extreme disease prevalence. The structure reveals a cross-β architecture assembled from two 76-residue long proto-filaments. Despite >70% sequence homology to mouse and human SAA, the cat SAA variant adopts a distinct amyloid fold. Inclusion of an eight-residue insert unique to feline SAA contributes to increased amyloid stability. The presented feline AA amyloid structure is fully compatible with the 99% identical amino acid sequence of amyloid fragments of captive cheetah.
History
DepositionApr 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum amyloid A protein
B: Serum amyloid A protein
C: Serum amyloid A protein
D: Serum amyloid A protein
E: Serum amyloid A protein
F: Serum amyloid A protein
G: Serum amyloid A protein
H: Serum amyloid A protein
I: Serum amyloid A protein
J: Serum amyloid A protein


Theoretical massNumber of molelcules
Total (without water)144,49810
Polymers144,49810
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Serum amyloid A protein / Serum amyloid A


Mass: 14449.766 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Felis catus (domestic cat) / References: UniProt: Q1T770

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: AA amyloid extracted from kidney of deceased cat / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Felis catus (domestic cat) / Organ: kidney
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow discharged for 30s at 30mA using a GloQube system
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2652 / Details: images takes for analysis

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPU2.8image acquisitionautomatic collection
4CTFFIND4CTF correction
7Coot0.8.2model fitting
8ISOLDE1.1.0model fitting
9UCSF ChimeraX1.1.1model fitting
11PHENIX1.19model refinement
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.29627 ° / Axial rise/subunit: 4.9043 Å / Axial symmetry: C2
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65000 / Symmetry type: HELICAL
Atomic model buildingB value: 76.7 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026320
ELECTRON MICROSCOPYf_angle_d0.8168530
ELECTRON MICROSCOPYf_dihedral_angle_d11.4142170
ELECTRON MICROSCOPYf_chiral_restr0.048740
ELECTRON MICROSCOPYf_plane_restr0.0111150

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